Multi-photon microscopy is suitable for high resolution and long term imaging of living tissues. It allows investigation of local environment in femtoliter volumes deep in tissues, thanks to its intrinsic three-dimensional resolution, high penetration depth, negligible out-of-focus photobleaching and (Helmchen 2005). minimal photo damage and phototoxicity (Denk 1990; Squirrell 1999; Zipfel 2003; Zipfel 2003). Auto-fluorescence in live tissues arises from endogenous proteins and physiologically relevant fluorophores such as collagen, elastin, porphyrin, retinoids, flavins, nicotinamide adenine dinucleotide, hemoglobin and serotonin (Zipfel 2003). NADH and FAD are the main metabolic coenzymes involved in oxidative phosphorylation and glycolysis and they report on metabolic changes associated with cell carcinogenesis and differentiation (Smith 2000; Skala 2007) while retinoid signaling is involved in differentiation of stem and precursor cells and embryonic development (Durston 1989; Bowles 2006). Two-photon excited fluorescence alone cannot assign auto-fluorescence signal to specific intrinsic molecular sources.
Additional methods have been proposed to assign autofluorescence to specific tissue components, but with limited success. Principal component analysis of emission spectra requires additional information on the tissue biochemical composition and can only separate a limited number of tissue components. The discrimination between intrinsic fluorescence sources by emission wavelength is also limited by the overlapping of emission spectra of different fluorescent species, such as NADPH and NADH (Huang 2002). Multi-exponential fitting of complex fluorescence intensity decays is based on a fitting procedure that requires assumptions on the biological tissues, where multiple fluorescent species are present in the focal volume. Several fluorophores and proteins are characterized by conformational heterogeneity and have complex lifetime distribution with more than one exponential component (Alcala 1987; Wouters 2001; Peter 2004). Moreover non-exponential processes such as energy transfer (FRET), pH variation, scattering and quenching often occur in tissues. Hence the choice of a decay model for the intensity decay fitting is arbitrary and it difficult to associate specific tissue components to exponential decays (Verveer 2000; Pelet 2004; Medine 2007).